[gmx-users] Freeze group atoms changing position

[Justin Lemkul]

On 11/1/12 4:56 PM, Alex Marshall wrote:
> I've created a position restraint file for the specific waters that I need
> to immobilize, but I'm having a hard time getting grompp to apply it
> successfully. No matter where I put #include "posre.itp" in my topology
> file grompp returns fatal errors about the atomic indices being out of
> bounds. Is it actually possible to only apply position restraints to some
> molecules within a species and leave the rest alone?
>

Yes, but you can't simply #include "spc.itp" and then call the position 
restraint file, for example.  You need a [moleculetype] for the entire block of 
water, since position restraints can only be applied per [moleculetype].

-Justin

> On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/31/12 3:55 PM, Alex Marshall wrote:
>>
>>> Chris, is that for freeze groups or position restraints?
>>>
>>>
>> I will assume Chris was referring to the restraint method - you need an
>> index file for creating the position restraint .itp file using genrestr.
>>   It will save you a ton of time over doing it manually.
>>
>> -Justin
>>
>>
>>   On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale <
>>> chris.neale at mail.utoronto.ca> wrote:
>>>
>>>   No need to rename... just make an .ndx group.
>>>>
>>>> -- original message --
>>>>
>>>> As I understand it, position restraints for an atom are set in the
>>>> topology
>>>> file and applied to that atom in each of that species. In order to
>>>> restrain
>>>> some but not all of the water I'd have to copy the topology of my water
>>>> model and add the restraints, then rename (and group together) the atoms
>>>> I
>>>> want to freeze so that they're identified with the appropriate topology
>>>> file. Does this sound like it would work? Is there some other way that
>>>> you
>>>> might do it?
>>>>
>>>> Thanks
>>>>
>>>> On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall <amarsh59 at uwo.ca>
>>>> wrote:
>>>>
>>>>   Justin: I'll try using position restraints instead of freezing the water
>>>>> in the tube. Thanks for the tip.
>>>>>
>>>>> Bogdan: I don't think I'm using constraints other than freeze groups. I
>>>>> wasn't using energy group exclusions though. I tried running the
>>>>>
>>>> simulation
>>>>
>>>>> from the same initial configuration with newly-defined energy groups
>>>>> CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second
>>>>> for
>>>>> the free atoms. The list of exclusions reads:
>>>>> energygrp_excl           = CNT_GRA_WAL_IN CNT_GRA_WAL_IN
>>>>>
>>>>> Long story short, I'm roughly 15 ns into the simulation and the same two
>>>>> waters have jumped. I'll check the manual again though. Thanks.
>>>>>
>>>>> On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu <bcostescu at
>>>>>
>>>> gmail.com>wrote:
>>>>
>>>>>
>>>>>   On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall <amarsh59 at uwo.ca>
>>>>>>
>>>>> wrote:
>>>>
>>>>> Thanks Justin. I identified the offending waters using vmd (adding 1
>>>>>>>
>>>>>> to
>>>>
>>>>> resID and atom number since vmd starts counting at 0) and checked
>>>>>>> confout.gro to make sure the coordinates matched up. I only have one
>>>>>>>
>>>>>> group
>>>>>>
>>>>>>> for all frozen atoms in the system, and these guys are definitely in
>>>>>>>
>>>>>> it.
>>>>
>>>>>
>>>>>> Are you using some kind of constraints ? Are you using energy group
>>>>>> exclusions to avoid interactions between frozen atoms ? If you search
>>>>>> the manual for "frozen" you'll find some warnings and recommendations.
>>>>>>
>>>>>> Cheers,
>>>>>> Bogdan
>>>>>> --
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Alex Marshall
>>>>> M.Sc. Candidate
>>>>> Department of Applied Mathematics
>>>>> The University of Western Ontario
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> Alex Marshall
>>>> M.Sc.
>>>> Department of Applied Mathematics
>>>> The University of Western Ontario
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>
>>>>
>>>
>>>
>>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================